This research presents a bottom-up methodology for assessing biogas potentials applied in a local community in Croatia. The research is based on analysing the flow of resources on a local level and capability of local actors to innovate and cooperate. Our method grades the local actors – in this case, owners of family farms in Gundinci municipality in Croatia – based on their farms’ biogas potential (or the amount and quality of manure they produce) and an indicator which we refer to as innovative-cooperation capacity. This methodology builds upon the biogas potential analysis by identifying farmers who are willing to improve their farms manure management system and cooperate in the field of biogas production in Gundinci. The replication of this methodology could stimulate rural development, through pinpointing realizable biogas projects, which could generate new money flows for the local economies and help farmers meet the norms of the European Union Nitrates Directive which regulates manure management, in order to control nitrogen flows in agriculture.